Colonial subjects who choose to cooperate are often given a reward or status not otherwise given under the old rule. This was a common tactic of the British--pull underclasses into the military and/or government rule. By doing this, you get support, it is cost effective as the colony will govern itself, and you lessen the power of the old elite.
The old elite are more likely to react with violence or rejection of the colonial system. They are typically more equipped to fight against the colonial power. Additionally, members of the military, if replaced, may also rebel against the colonial power. Another factor contributing to rebellion, may be the removal of important traditions or religious rites.